West, Robert B
Online Publication Date2015-05-06
Print Publication Date2015-12
Permanent link to this recordhttp://hdl.handle.net/10754/596784
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AbstractSomatic variants can be used as lineage markers for the phylogenetic reconstruction of cancer evolution. Since somatic phylogenetics is complicated by sample heterogeneity, novel specialized tree-building methods are required for cancer phylogeny reconstruction. We present LICHeE (Lineage Inference for Cancer Heterogeneity and Evolution), a novel method that automates the phylogenetic inference of cancer progression from multiple somatic samples. LICHeE uses variant allele frequencies of somatic single nucleotide variants obtained by deep sequencing to reconstruct multi-sample cell lineage trees and infer the subclonal composition of the samples. LICHeE is open source and available at http://viq854.github.io/lichee .
CitationPopic V, Salari R, Hajirasouliha I, Kashef-Haghighi D, West RB, et al. (2015) Fast and scalable inference of multi-sample cancer lineages. Genome Biology 16. Available: http://dx.doi.org/10.1186/s13059-015-0647-8.
SponsorsAuthors would like to thank Arend Sidow for valuable discussions and Aaron C. Abajian for contributing to the simulation studies. VP was supported by the Stanford-KAUST grant. RS and IH were also supported by Natural Sciences and Engineering Research Council of Canada (NSERC) Postdoctoral Fellowships. DK was supported by an STMicroelectronics Stanford Graduate Fellowship. This work was funded by a grant from KAUST to SB.
PubMed Central IDPMC4501097
CollectionsPublications Acknowledging KAUST Support
- BAMSE: Bayesian model selection for tumor phylogeny inference among multiple samples.
- Authors: Toosi H, Moeini A, Hajirasouliha I
- Issue date: 2019 Jun 6
- Using LICHeE and BAMSE for Reconstructing Cancer Phylogenetic Trees.
- Authors: Ricketts C, Popic V, Toosi H, Hajirasouliha I
- Issue date: 2018 Jun
- PhyloWGS: reconstructing subclonal composition and evolution from whole-genome sequencing of tumors.
- Authors: Deshwar AG, Vembu S, Yung CK, Jang GH, Stein L, Morris Q
- Issue date: 2015 Feb 13
- Clonality Inference from Single Tumor Samples Using Low-Coverage Sequence Data.
- Authors: Donmez N, Malikic S, Wyatt AW, Gleave ME, Collins CC, Sahinalp SC
- Issue date: 2017 Jun
- Inferring clonal evolution of tumors from single nucleotide somatic mutations.
- Authors: Jiao W, Vembu S, Deshwar AG, Stein L, Morris Q
- Issue date: 2014 Feb 1